Merge branch 'main' into pet-nc

Author: ceriottm

examples/periodic-hamiltonian/environment.yml

@@ -11,13 +11,7 @@ dependencies:
       - ase==3.22.1
       - seekpath
       - requests
-      - metatensor
-      - metatensor-core
-      - metatensor-learn
-      - metatensor-operations
-      - metatensor-torch
-      - --extra-index-url https://download.pytorch.org/whl/cpu 
-      - rascaline-torch @ git+https://github.com/luthaf/rascaline@3450bc4d609aee87ab73648b059536baa97d15ac#subdirectory=python/rascaline-torch
+      - --extra-index-url https://download.pytorch.org/whl/cpu
       - lightning
       - xitorch
       - keras_core

examples/pet-mad/environment.yml

@@ -4,11 +4,10 @@ channels:
 dependencies:
   - python=3.12
   - lammps-metatensor=*=cpu*nompi*
-  - libtorch=*=cpu*mkl*  
   - pet-mad
   - pip
   - pip:
     - ase
-    - ipi>=3.1.r21
+    - ipi>=3.1.2
     - chemiscope>=0.8.4  
     - matplotlib

examples/pet-mad/pet-mad.py

@@ -140,6 +140,13 @@
 
 calculator = PETMADCalculator(version="latest", device="cpu")
 
+# %%
+#
+# The model can also be exported in a format that can be used with
+# external MD engines. This is done by saving the model to a file,
+# which includes the model architecture and weights.
+
+calculator.model.save("pet-mad-latest.pt")
 
 # %%
 #
@@ -380,19 +387,6 @@
 # without having to introduce vacancies or wait for the
 # very long time scale needed for diffusion.
 
-# %%
-#
-# Before starting the simulations with MD engines, it is important
-# to export the model to a format that can be used by the engine.
-# This is done by saving the model to a file, which includes the
-# model weights and the compiled extensions. We use the ``collect_extensions``
-# argument to save the compiled extensions to disk. These extensions ensure that
-# the model remains self-contained and can be executed without requiring the
-# original Python or C++ source code. In particular, this is necessary for
-# the LAMMPS interface to work because it has no access to the Python code.
-
-calculator.model.save("pet-mad-latest.pt", collect_extensions="extensions")
-
 
 # %%
 #
@@ -513,7 +507,7 @@
 
 ase.io.write("al6xxx-o2.data", al_surface, format="lammps-data", masses=True)
 
-subprocess.check_call(["lmp_serial", "-in", "data/al6xxx-o2.in"])
+subprocess.check_call(["lmp", "-in", "data/al6xxx-o2.in"])
 
 # %%
 #